Two new Pokémon Nintendo 3DS themes have been released in Japan:
- Pokémon: A Sinister Organization - Team Aqua
- Pokémon: A Sinister Organization - Team Magma

The "A Sinister Organization - Team Aqua" theme feature artwork of Team Aqua Grunts, Admins, Boss and Primal Kyogre.
The background music is the "Battle! Team Aqua" music from Pokémon Omega Ruby and Alpha Sapphire.
This theme is available for 200 yen.

The "A Sinister Organization - Team Magma" theme feature artwork of Team Aqua Grunts, Admins, Boss and Primal Groudon.
The background music is the "Battle! Team Magma" music from Pokémon Omega Ruby and Alpha Sapphire.
This theme is available for 200 yen.